Contacts of the helix formed by residues 97 - 113 (chain C) in PDB entry 2W2X
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ARG 97 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77C PHE* 3.8 1.8 - - - -
95C THR* 3.0 13.2 + - - -
96C ASP* 1.3 103.6 + - + +
98C VAL* 1.3 58.8 + - - +
99C GLU* 3.4 22.0 - - + +
100C GLU* 2.7 64.2 + - - +
101C LEU 3.3 0.2 + - - -
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Residues in contact with VAL 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B VAL* 3.6 30.3 - - + -
37B PHE* 4.7 3.4 - - + -
64B TYR* 4.4 13.9 - - + -
67B LEU* 3.8 20.0 - - + -
77C PHE* 3.3 41.1 - - + -
97C ARG* 1.3 72.0 - - - +
99C GLU* 1.3 77.6 + - - +
100C GLU 3.1 0.2 + - - -
101C LEU* 3.3 9.4 + - + +
102C PHE* 2.9 26.2 + - - +
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Residues in contact with GLU 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B ARG* 4.6 16.5 - - - +
67B LEU* 4.7 7.1 + - - -
70B LEU* 4.2 18.6 - - + +
97C ARG* 3.4 28.7 - - + +
98C VAL* 1.3 90.5 + - - +
100C GLU* 1.3 64.8 + - - +
102C PHE* 3.8 8.4 - - - +
103C GLU* 3.3 36.1 + - - +
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Residues in contact with GLU 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C GLU 6.1 1.3 - - - +
95C THR* 3.7 16.7 - - + -
96C ASP* 4.0 5.4 + - - +
97C ARG* 2.7 80.0 + - - +
99C GLU* 1.3 73.7 - - - +
101C LEU* 1.3 55.2 + - - +
102C PHE 3.1 1.3 + - - -
103C GLU* 3.2 12.4 + - + +
104C TRP* 2.6 47.9 + - + +
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Residues in contact with LEU 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B VAL* 5.6 2.5 - - + -
37B PHE* 4.4 3.4 - - + -
67C LYS* 3.9 28.7 - - + -
68C ALA 5.7 1.1 - - - +
76C SER 5.1 0.4 - - - +
77C PHE* 3.5 38.1 - - + +
78C VAL 3.8 32.1 - - - +
79C PHE* 3.9 20.2 - - + +
95C THR* 3.5 18.3 + - + +
97C ARG 3.3 2.2 + - - -
98C VAL* 3.4 14.4 - - + +
100C GLU* 1.3 78.5 - - - +
102C PHE* 1.3 62.9 + - - +
104C TRP* 4.5 2.2 - - - +
105C PHE* 2.9 29.9 + - + +
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Residues in contact with PHE 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B PHE* 3.6 34.3 - + + -
56B TRP* 4.2 9.9 - + - -
67B LEU* 3.7 26.5 - - + -
70B LEU* 4.0 38.4 - - + -
71B SER* 3.8 18.8 - - - -
98C VAL 2.9 15.9 + - - +
99C GLU* 3.8 7.6 - - - +
100C GLU 3.1 0.2 - - - -
101C LEU* 1.3 76.2 - - - +
103C GLU* 1.3 77.2 + - + +
105C PHE* 3.7 1.0 - - - +
106C GLN* 3.0 55.4 + - + +
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Residues in contact with GLU 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B LEU* 5.1 13.5 - - - +
8C GLN* 4.4 21.4 + - - +
99C GLU* 3.3 33.5 + - - +
100C GLU* 3.2 20.3 + - + +
102C PHE* 1.3 93.2 - - + +
104C TRP* 1.9 57.8 + - + +
106C GLN* 3.6 4.6 - - - +
107C SER* 3.1 22.2 + - - -
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Residues in contact with TRP 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C GLN* 3.2 32.5 + - + -
9C GLN* 3.5 30.9 + - - -
10C GLY* 3.6 14.0 - - - -
11C GLU 4.8 1.6 + - - -
12C LEU* 3.7 34.2 - - + +
27C CYS* 3.7 26.9 - - + -
28C ALA* 4.2 2.9 - - - -
29C ILE* 3.6 28.7 - - + -
34C LEU* 4.0 12.8 - - + -
35C SER 4.2 1.8 - - - -
79C PHE* 3.8 17.5 - + + -
95C THR* 5.2 0.2 - - + -
100C GLU* 2.6 48.1 + - + +
101C LEU* 4.1 1.8 - - - +
103C GLU* 1.9 50.1 - - + +
105C PHE* 1.3 58.9 + - - +
107C SER* 3.2 4.3 + - - -
108C ILE* 2.9 43.7 + - + +
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Residues in contact with PHE 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B PHE* 3.7 26.2 - + + -
38B ASP* 5.4 4.7 - - - -
39B ASN* 4.2 15.0 - - + -
65C VAL* 3.5 38.1 - - + +
66C VAL* 4.1 1.1 - - - -
67C LYS* 3.7 41.5 - - + -
79C PHE* 4.4 8.2 - - + -
101C LEU* 2.9 23.6 + - + +
102C PHE 3.7 1.8 - - - +
104C TRP* 1.3 77.4 - - - +
106C GLN* 1.3 62.9 + - - +
108C ILE* 3.1 3.3 + - - +
109C ARG* 2.7 58.9 + - + +
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Residues in contact with GLN 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B PHE* 3.5 22.6 - - - -
39B ASN* 2.7 24.6 + - - +
56B TRP* 3.8 14.0 - - + -
102C PHE* 3.0 49.0 + - + +
103C GLU* 3.9 4.5 - - - +
105C PHE* 1.3 79.2 - - - +
107C SER* 1.3 56.8 - - - +
109C ARG* 2.4 40.6 + - - +
110C GLU* 2.8 35.7 + - - +
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Residues in contact with SER 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C GLN* 3.8 31.0 - - - -
29C ILE* 4.1 7.2 - - - -
103C GLU 3.1 13.7 + - - -
104C TRP 3.5 8.5 - - - -
106C GLN* 1.3 77.0 - - - +
108C ILE* 2.1 47.2 - - - +
110C GLU* 3.7 9.4 - - - +
111C ILE* 3.2 34.3 + - - +
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Residues in contact with ILE 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C ILE* 4.1 17.3 - - + -
34C LEU* 4.3 7.2 - - + -
60C LEU* 3.8 26.2 - - + -
63C TYR* 6.2 0.2 - - + -
65C VAL* 3.2 23.6 - - + +
79C PHE* 3.3 41.5 - - + -
81C LEU* 4.2 8.3 - - + -
104C TRP* 2.9 25.7 + - + +
105C PHE 4.0 1.1 - - - +
107C SER* 2.1 52.1 - - - +
109C ARG* 1.3 55.7 + - - +
111C ILE* 2.8 11.4 + - - +
112C THR* 2.8 43.1 + - + +
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Residues in contact with ARG 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ASN* 3.2 36.8 - - - +
40B TYR 5.7 1.8 + - - -
56B TRP* 4.1 14.3 - - - +
65C VAL* 3.5 14.7 - - + +
105C PHE* 2.7 41.1 + - + +
106C GLN* 2.4 43.0 + - - +
108C ILE* 1.3 76.8 - - - +
110C GLU* 1.3 70.4 + - - +
112C THR* 3.2 2.4 + - - -
113C TRP* 3.0 58.6 + - + +
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Residues in contact with GLU 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C GLN 2.8 21.8 + - - +
107C SER* 3.7 12.6 - - - +
109C ARG* 1.3 81.9 - - - +
111C ILE* 1.3 61.3 + - - +
113C TRP* 3.4 18.9 - - - +
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Residues in contact with ILE 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C ILE* 3.8 23.3 - - + -
31C ASP 3.8 21.3 - - - +
32C ALA* 3.8 16.2 - - + -
60C LEU* 3.8 36.1 - - + -
61C ASN* 4.9 7.6 - - - +
107C SER* 3.2 26.4 + - - +
108C ILE* 2.8 12.8 + - - +
110C GLU* 1.3 80.1 - - - +
112C THR* 1.3 60.0 + - + +
113C TRP 3.5 4.0 + - - +
114C LYS* 4.8 4.7 - - - +
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Residues in contact with THR 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C LEU* 3.6 15.0 - - - +
61C ASN* 6.1 1.3 - - - +
63C TYR* 3.2 32.7 - - + +
64C ASN* 4.3 14.6 + - - -
65C VAL* 3.8 11.1 + - + +
84C LYS* 5.7 2.8 + - - -
108C ILE* 2.8 38.1 + - + +
109C ARG* 3.2 15.1 + - - -
111C ILE* 1.3 76.5 - - + +
113C TRP* 1.3 66.4 + - - +
114C LYS* 3.7 3.0 + - - -
115C ILE 5.7 0.3 - - - +
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Residues in contact with TRP 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A ARG* 6.0 4.7 - - - -
39B ASN* 5.4 6.1 - - + -
40B TYR* 4.7 4.7 - - - -
41B SER* 3.1 44.6 - - - -
109C ARG* 3.0 59.7 + - + +
110C GLU* 3.4 15.4 - - - +
111C ILE 3.3 0.7 - - - +
112C THR* 1.3 82.8 + - - +
114C LYS* 1.3 68.3 + - - +
115C ILE* 4.2 17.6 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il